[miso-users] error in testing sashimi_plot

Fri Apr 20 12:24:49 EDT 2018

Hello,

I think there is a major issue with sashimi_plot version vs miso version.

TL;DR: sashimi_plot need ".miso" files, which are removed by "miso_pack" function since Miso 0.5.0.

In fact miso_pack will pick up all the .miso files under each chr* folder and put them into a .miso_db file, and remove those .miso files.

Temporary solution: Make a copy of ".miso" files right after miso --run. According to the manual miso_zip will also pack the files if that's not done already.

Now to answer Jermaine Jenkins:

You are probably using a different version of Miso, and the test files are partially missing and / or files structure is not correct.

In my legace files of miso 0.4.9, the test-data/miso-data contains folders

"heartWT1", "heartWT2", "heartKOa", "heartKOb"

and under each of those folders there is a file named "chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:-.miso"

When I run my current miso/sashimi package (miso 0.5.3) on those test data, everything is OK and I got my output as in the manual.

>From the setting files, and from the flow of the analysis, I would assume that you need 4 bam files (one for each sample) and 4 miso output folders. Thus you need 4 .miso files for the test. Except in my 0.5.3 test files I have just one .miso file under /miso-data . When I do the test on that set of test data, I got the sashimi plot without BF intervals on the right of the output.

Questions to developpers:

When I tried to download from the git https://github.com/yarden/MISO/zipball/fastmiso it seems to point to miso0.4.9 (file name yarden-MISO-1ca049f).

Can you confirm that pip / last commit on git / zip download all point to the same version?

Is there a more recent version of sashimi plot that no longer relies on .miso files but on .miso_db files? On the current git the test files still contain .miso files, so I wonder if sashimi plot is ever updated since Miso 0.5.0. In fact, the miso_pack is released within Miso 0.5.0 during Feb 20, 2014, while the last sashimi_plot update was in Feb 11 2014. On the git, the last commit on sashimi_plot is Feb 23 2014 while the last commit on Miso is Aug 2017 in the same time of Miso 0.5.4.

Delong

________________________________
From: miso-users-bounces at mit.edu <miso-users-bounces at mit.edu> on behalf of Jermaine Jenkins <jljbbc88 at gmail.com>
Sent: April 9, 2018 7:58:08 PM
To: miso-users at mit.edu
Subject: [miso-users] error in testing sashimi_plot

Hi,

Whe trying to test sashimi_plot I am getting a errors and a plot without MISO estimates? Any help is appreciated.

Thanks,
JJ

part of the terminal output (full output is attached)

miso_prefix: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data
Searching for MISO files in: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT1
  - Looking for chromosome chr17 directories
Error: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT1 not a directory.
Error: Could not find MISO output files for sample heartWT1 (after searching in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT1 and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT2
  - Looking for chromosome chr17 directories
Error: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT2 not a directory.
Error: Could not find MISO output files for sample heartWT2 (after searching in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartWT2 and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOa
  - Looking for chromosome chr17 directories
Error: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOa not a directory.
Error: Could not find MISO output files for sample heartKOa (after searching in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOa and its subdirectories). Are you sure MISO output files are present in that directory?
Searching for MISO files in: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOb
  - Looking for chromosome chr17 directories
Error: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOb not a directory.
Error: Could not find MISO output files for sample heartKOb (after searching in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-data/miso-data/heartKOb and its subdirectories). Are you sure MISO output files are present in that directory?
Reading dimensions from settings...
 - Height: 5.00
 - Width: 7.00
Plotting read densities and MISO estimates along event...
  - Event: chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:-
Setting up plot using dimensions:  [7.0, 5.0]
Using intron scale  30.0
Using exon scale  4.0
Reading sample label: heartWT1.sorted.bam
Processing BAM: ./test-data/bam-data/heartWT1.sorted.bam
Warning: MISO file  not found
Loading MISO file:
Posterior plot failed.
Reading sample label: heartWT2.sorted.bam
Processing BAM: ./test-data/bam-data/heartWT2.sorted.bam
Warning: MISO file  not found
Loading MISO file:
Posterior plot failed.
Reading sample label: heartKOa.sorted.bam
Processing BAM: ./test-data/bam-data/heartKOa.sorted.bam
Warning: MISO file  not found
Loading MISO file:
Posterior plot failed.
Reading sample label: heartKOb.sorted.bam
Processing BAM: ./test-data/bam-data/heartKOb.sorted.bam
Warning: MISO file  not found
Loading MISO file:
Posterior plot failed.
Saving plot to: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/sashimi_plot/test-plot/chr17:45816186:45816265:- at chr17:45815912:45815950:- at chr17:45814875:45814965:-.pdf
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